# HG changeset patch
# User galaxyp
# Date 1502283494 14400
# Node ID 974dec16eb84ee1cbe40ab6a4602bb8dd5946728
# Parent  566046627ebfc420ddb24fa71a8f574bb930747b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

diff -r 566046627ebf -r 974dec16eb84 OpenSwathRTNormalizer.xml
--- a/OpenSwathRTNormalizer.xml	Wed Mar 01 12:16:05 2017 -0500
+++ b/OpenSwathRTNormalizer.xml	Wed Aug 09 08:58:14 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [Targeted Experiments]-->
-<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.1.0">
+<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.2.0">
   <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
@@ -65,7 +65,12 @@
   -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+  #end if
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
   -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
@@ -80,13 +85,23 @@
   -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+  #end if
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
   -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:method
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+  #end if
 #end if
 #if $param_algorithm_DIAScoring_dia_extraction_window:
   -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
@@ -110,7 +125,12 @@
   -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
 #end if
 #if $param_outlierDetection_outlierMethod:
-  -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
+  -outlierDetection:outlierMethod
+  #if " " in str($param_outlierDetection_outlierMethod):
+    "$param_outlierDetection_outlierMethod"
+  #else
+    $param_outlierDetection_outlierMethod
+  #end if
 #end if
 #if $param_outlierDetection_useIterativeChauvenet:
   -outlierDetection:useIterativeChauvenet
@@ -159,10 +179,18 @@
   -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
-  -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+  -algorithm:TransitionGroupPicker:background_subtraction
+  #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
+    "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
+  #else
+    $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+  #end if
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
-  -algorithm:TransitionGroupPicker:recalculate_peaks     "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
+  -algorithm:TransitionGroupPicker:recalculate_peaks
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors:
+  -algorithm:TransitionGroupPicker:use_precursors
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
   -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
@@ -171,7 +199,7 @@
   -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
-  -algorithm:TransitionGroupPicker:compute_peak_quality     "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
+  -algorithm:TransitionGroupPicker:compute_peak_quality
 #end if
     #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
   -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
@@ -189,38 +217,91 @@
   -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
 #end if
     #if $adv_opts.param_algorithm_Scores_use_shape_score:
-  -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score
+  -algorithm:Scores:use_shape_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
+    "$adv_opts.param_algorithm_Scores_use_shape_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_shape_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_coelution_score:
-  -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score
+  -algorithm:Scores:use_coelution_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
+    "$adv_opts.param_algorithm_Scores_use_coelution_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_coelution_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_rt_score:
-  -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score
+  -algorithm:Scores:use_rt_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
+    "$adv_opts.param_algorithm_Scores_use_rt_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_rt_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_library_score:
-  -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score
+  -algorithm:Scores:use_library_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
+    "$adv_opts.param_algorithm_Scores_use_library_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_library_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
-  -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score
+  -algorithm:Scores:use_elution_model_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
+    "$adv_opts.param_algorithm_Scores_use_elution_model_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_elution_model_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_intensity_score:
-  -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score
+  -algorithm:Scores:use_intensity_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
+    "$adv_opts.param_algorithm_Scores_use_intensity_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_intensity_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
-  -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+  -algorithm:Scores:use_nr_peaks_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
+    "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
-  -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score
+  -algorithm:Scores:use_total_xic_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
+    "$adv_opts.param_algorithm_Scores_use_total_xic_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_total_xic_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_sn_score:
-  -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score
+  -algorithm:Scores:use_sn_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
+    "$adv_opts.param_algorithm_Scores_use_sn_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_sn_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_dia_scores:
-  -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores
+  -algorithm:Scores:use_dia_scores
+  #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
+    "$adv_opts.param_algorithm_Scores_use_dia_scores"
+  #else
+    $adv_opts.param_algorithm_Scores_use_dia_scores
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
   -algorithm:Scores:use_ms1_correlation
 #end if
+    #if $adv_opts.param_algorithm_Scores_use_sonar_scores:
+  -algorithm:Scores:use_sonar_scores
+#end if
     #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
   -algorithm:Scores:use_ms1_fullscan
 #end if
@@ -305,24 +386,11 @@
         <option value="smoothed">smoothed</option>
         <option value="original">original</option>
       </param>
-      <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
+      <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
+      <param name="param_algorithm_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
       <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
       <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
-      <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
+      <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
       <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>
       <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>
       <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
@@ -364,11 +432,12 @@
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
       </param>
-      <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) ">
+      <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) If turned off, will not use fragment ion spectra for scoring">
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
       </param>
       <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
+      <param name="param_algorithm_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
       <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>
       <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
     </expand>
diff -r 566046627ebf -r 974dec16eb84 datatypes_conf.xml
--- a/datatypes_conf.xml	Wed Mar 01 12:16:05 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<datatypes>
-  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
-    <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/>
-    <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/>
-    <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/>
-    <datatype extension="grid" type="galaxy.datatypes.data:Grid"/>
-    <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/>
-    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
-    <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-  </registration>
-</datatypes>
diff -r 566046627ebf -r 974dec16eb84 filetypes.txt
--- a/filetypes.txt	Wed Mar 01 12:16:05 2017 -0500
+++ b/filetypes.txt	Wed Aug 09 08:58:14 2017 -0400
@@ -14,7 +14,7 @@
 consensusXML  consensusxml      galaxy.datatypes.proteomics:ConsensusXML    application/xml
 edta          tabular           galaxy.datatypes.tabular:Tabular 
 featureXML    featurexml        galaxy.datatypes.proteomics:FeatureXML      application/xml
-idXML         idxml             galaxy.datatypes.proteomics:IdXM            application/xml
+idXML         idxml             galaxy.datatypes.proteomics:IdXML           application/xml
 mzML          mzml              galaxy.datatypes.proteomics:MzML            application/xml
 mzXML         mzxml             galaxy.datatypes.proteomics:MzXML           application/xml
 pepXML        pepxml            galaxy.datatypes.proteomics:PepXml          application/xml
@@ -26,4 +26,4 @@
 msp           msp               galaxy.datatypes.proteomics:Msp
 mzid          mzid              galaxy.datatypes.proteomics:MzIdentML       application/xml
 png           png               galaxy.datatypes.images:Png                 image/png
-mgf           mgf               galaxy.datatypes.proteomics:Mgf
\ No newline at end of file
+mgf           mgf               galaxy.datatypes.proteomics:Mgf
diff -r 566046627ebf -r 974dec16eb84 macros.xml
--- a/macros.xml	Wed Mar 01 12:16:05 2017 -0500
+++ b/macros.xml	Wed Aug 09 08:58:14 2017 -0400
@@ -2,7 +2,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.1">openms</requirement>
+      <requirement type="package" version="2.2">openms</requirement>
       <requirement type="package" version="15.12.15.2">xtandem</requirement>
       <requirement type="package" version="1.0">fido</requirement>
       <requirement type="package" version="2016.10.26">msgf_plus</requirement>
diff -r 566046627ebf -r 974dec16eb84 readme.md
--- a/readme.md	Wed Mar 01 12:16:05 2017 -0500
+++ b/readme.md	Wed Aug 09 08:58:14 2017 -0400
@@ -14,15 +14,29 @@
 Generating OpenMS wrappers
 ==========================
 
- * install OpenMS (you can do this automatically through the Tool Shed)
+ * install OpenMS (you can do this automatically through Conda)
  * create a folder called CTD
- * inside of your new installed openms/bin folder, execute the following command:
+ * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
     
     ```bash
     for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
     ```
     
- * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
+ * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
+ 
+    ```bash
+    ls >> tools.txt
+    ```
+    
+ * search for the `bin` folder of your conda environment containing OpenMS and do:
+ 
+    ```bash
+    while read p; do
+        ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
+    done <tools.txt
+    ```
+    
+ * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
 
  * clone or install CTDopts
 
@@ -39,10 +53,10 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/blankclemens/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. 
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
 
     ```bash
     python generator.py \ 
@@ -102,17 +116,32 @@
     [...]
     ]]>
     ```
- * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
+    
+ * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
  
-        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
-     
-   and change it to
+   ```
+    <command><![CDATA[
    
-        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
+      ## check input file type
+      #set $in_type = $param_in.ext
+
+      ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+      ln -s '$param_in' 'param_in.${in_type}' &&
+
+      IDFileConverter
 
- * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
+      #if $param_in:
+        -in 'param_in.${in_type}'
+      #end if
+
+        [...]
+        ]]>
+    ```
+
+ * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
  
-        <data name="param_out" metadata_source="param_in" auto_format="true"/>
+   - `<data name="param_out" auto_format="true"/>`
+   - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
         
  * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.
  
diff -r 566046627ebf -r 974dec16eb84 tool.conf
--- a/tool.conf	Wed Mar 01 12:16:05 2017 -0500
+++ b/tool.conf	Wed Aug 09 08:58:14 2017 -0400
@@ -6,13 +6,7 @@
     <tool file="openms/RTModel.xml"/>
     <tool file="openms/RTPredict.xml"/>
   </section>
-  <section id="section-id-DEFAULT" name="DEFAULT">
-    <tool file="openms/OpenSwathFileSplitter.xml"/>
-    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
-  </section>
   <section id="section-id-TargetedExperiments" name="Targeted Experiments">
-    <tool file="openms/ConvertTraMLToTSV.xml"/>
-    <tool file="openms/ConvertTSVToTraML.xml"/>
     <tool file="openms/InclusionExclusionListCreator.xml"/>
     <tool file="openms/MRMMapper.xml"/>
     <tool file="openms/OpenSwathAnalyzer.xml"/>
@@ -22,13 +16,17 @@
     <tool file="openms/OpenSwathDecoyGenerator.xml"/>
     <tool file="openms/OpenSwathDIAPreScoring.xml"/>
     <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
+    <tool file="openms/OpenSwathFileSplitter.xml"/>
+    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
     <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
     <tool file="openms/OpenSwathRTNormalizer.xml"/>
     <tool file="openms/PrecursorIonSelector.xml"/>
+    <tool file="openms/TargetedFileConverter.xml"/>
   </section>
   <section id="section-id-Utilities" name="Utilities">
     <tool file="openms/AccurateMassSearch.xml"/>
     <tool file="openms/CVInspector.xml"/>
+    <tool file="openms/DatabaseFilter.xml"/>
     <tool file="openms/DecoyDatabase.xml"/>
     <tool file="openms/DeMeanderize.xml"/>
     <tool file="openms/Digestor.xml"/>
@@ -44,7 +42,6 @@
     <tool file="openms/LabeledEval.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
-    <tool file="openms/MapAlignmentEvaluation.xml"/>
     <tool file="openms/MassCalculator.xml"/>
     <tool file="openms/MetaboliteSpectralMatcher.xml"/>
     <tool file="openms/MetaProSIP.xml"/>
@@ -62,12 +59,14 @@
     <tool file="openms/QCMerger.xml"/>
     <tool file="openms/QCShrinker.xml"/>
     <tool file="openms/RNPxl.xml"/>
+    <tool file="openms/RNPxlSearch.xml"/>
     <tool file="openms/RNPxlXICFilter.xml"/>
     <tool file="openms/RTEvaluation.xml"/>
     <tool file="openms/SemanticValidator.xml"/>
     <tool file="openms/SequenceCoverageCalculator.xml"/>
     <tool file="openms/SimpleSearchEngine.xml"/>
     <tool file="openms/SpecLibCreator.xml"/>
+    <tool file="openms/SpectraSTSearchAdapter.xml"/>
     <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
     <tool file="openms/TICCalculator.xml"/>
     <tool file="openms/TopPerc.xml"/>
@@ -78,6 +77,7 @@
     <tool file="openms/ConsensusMapNormalizer.xml"/>
     <tool file="openms/FeatureLinkerLabeled.xml"/>
     <tool file="openms/FeatureLinkerUnlabeled.xml"/>
+    <tool file="openms/FeatureLinkerUnlabeledKD.xml"/>
     <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
     <tool file="openms/MapRTTransformer.xml"/>
   </section>
@@ -154,9 +154,7 @@
     <tool file="openms/FeatureFinderMultiplex.xml"/>
     <tool file="openms/FeatureFinderSuperHirn.xml"/>
     <tool file="openms/IsobaricAnalyzer.xml"/>
-    <tool file="openms/ITRAQAnalyzer.xml"/>
     <tool file="openms/ProteinQuantifier.xml"/>
     <tool file="openms/ProteinResolver.xml"/>
-    <tool file="openms/TMTAnalyzer.xml"/>
   </section>
 </toolbox>